Structure of PDB 8ph4 Chain A Binding Site BS01

Receptor Information

>8ph4 Chain A (length=301) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
S

Ligand information

• Ligand ID: YQN
• InChI: InChI=1S/C28H33N5O4/c1-28(2,3)19-11-13-21(14-12-19)33(26(36)22-17-30-27(37)32-24(22)34)23(18-8-7-15-29-16-18)25(35)31-20-9-5-4-6-10-20/h7-8,11-17,20,22-23H,4-6,9-10H2,1-3H3,(H,31,35)(H,32,34,37)/t22-,23-/m0/s1
• InChIKey: IZDUHWAQOVIQDS-GOTSBHOMSA-N
• SMILES:
  CACTVS 3.385: CC(C)(C)c1ccc(cc1)N([CH](C(=O)NC2CCCCC2)c3cccnc3)C(=O)[CH]4C=NC(=O)NC4=O
  OpenEye OEToolkits 2.0.7: CC(C)(C)c1ccc(cc1)N([C@@H](c2cccnc2)C(=O)NC3CCCCC3)C(=O)C4C=NC(=O)NC4=O
  OpenEye OEToolkits 2.0.7: CC(C)(C)c1ccc(cc1)N(C(c2cccnc2)C(=O)NC3CCCCC3)C(=O)C4C=NC(=O)NC4=O
  CACTVS 3.385: CC(C)(C)c1ccc(cc1)N([C@H](C(=O)NC2CCCCC2)c3cccnc3)C(=O)[C@H]4C=NC(=O)NC4=O
• Formula: C28 H33 N5 O4
• Name: ~{N}-(4-~{tert}-butylphenyl)-~{N}-[(1~{S})-2-(cyclohexylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-2,6-bis(oxidanylidene)-5~{H}-pyrimidine-5-carboxamide
• PDB chain: 8ph4 Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ph4 Targeting the Main Protease (M pro , nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.
• Resolution: 1.69 Å
• Binding residue (original residue number in PDB): G15 M17 W31 A70 G71 N72 V73 P96 K97
• Binding residue (residue number reindexed from 1): G15 M17 W31 A70 G71 N72 V73 P96 K97
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:8ph4, PDBe:8ph4, PDBj:8ph4
• PDBsum: 8ph4
• PubMed: 38232960
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)